X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueProperties.java;h=0b1b7cc943ba6d14aacdb10310d6108bfd004cb1;hb=a45b4529c64901e9e4b53b6c74ee804370c91002;hp=b4b545252d1d6506840527fc41b7437751031413;hpb=48e6a09db5cad4143d1b9fbebf1b6996fc95ed07;p=jalview.git diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java index b4b5452..0b1b7cc 100755 --- a/src/jalview/schemes/ResidueProperties.java +++ b/src/jalview/schemes/ResidueProperties.java @@ -20,11 +20,6 @@ */ package jalview.schemes; -import jalview.analysis.scoremodels.FeatureScoreModel; -import jalview.analysis.scoremodels.PIDScoreModel; -import jalview.analysis.scoremodels.ScoreMatrix; -import jalview.api.analysis.ScoreModelI; - import java.awt.Color; import java.util.ArrayList; import java.util.Arrays; @@ -37,8 +32,6 @@ import java.util.Vector; public class ResidueProperties { - public static Hashtable scoreMatrices = new Hashtable(); - // Stores residue codes/names and colours and other things public static final int[] aaIndex; // aaHash version 2.1.1 and below @@ -1246,16 +1239,6 @@ public class ResidueProperties propMatrixPos[i][i] = maxP; propMatrixEpos[i][i] = maxEP; } - // JAL-1512 comment out physicochemical score matrices for 2.8.1 release - // scoreMatrices.put("Conservation Pos", new - // ScoreMatrix("Conservation Pos",propMatrixPos,0)); - // scoreMatrices.put("Conservation Both", new - // ScoreMatrix("Conservation Both",propMatrixF,0)); - // scoreMatrices.put("Conservation EnhPos", new - // ScoreMatrix("Conservation EnhPos",propMatrixEpos,0)); - scoreMatrices.put("PID", new PIDScoreModel()); - scoreMatrices.put("Sequence Feature Similarity", - new FeatureScoreModel()); } private ResidueProperties() @@ -1282,11 +1265,6 @@ public class ResidueProperties return aa3Hash; } - public static float[][] getDNA() - { - return ResidueProperties.DNA; - } - public static float[][] getBLOSUM62() { return ResidueProperties.BLOSUM62; @@ -1297,24 +1275,6 @@ public class ResidueProperties return getPAM250(A1.charAt(0), A2.charAt(0)); } - public static float getBLOSUM62(char c1, char c2) - { - float pog = 0; - - try - { - int a = aaIndex[c1]; - int b = aaIndex[c2]; - - pog = ResidueProperties.BLOSUM62[a][b]; - } catch (Exception e) - { - // System.out.println("Unknown residue in " + A1 + " " + A2); - } - - return pog; - } - public static String codonTranslate(String lccodon) { String cdn = codonHash2.get(lccodon.toUpperCase()); @@ -1325,43 +1285,6 @@ public class ResidueProperties return cdn; } - public static float[][] getDefaultPeptideMatrix() - { - return ResidueProperties.getBLOSUM62(); - } - - public static float[][] getDefaultDnaMatrix() - { - return ResidueProperties.getDNA(); - } - - /** - * get a ScoreMatrix based on its string name - * - * @param pwtype - * @return matrix in scoreMatrices with key pwtype or null - */ - public static ScoreMatrix getScoreMatrix(String pwtype) - { - Object val = scoreMatrices.get(pwtype); - if (val != null && val instanceof ScoreMatrix) - { - return (ScoreMatrix) val; - } - return null; - } - - /** - * get a ScoreModel based on its string name - * - * @param pwtype - * @return scoremodel of type pwtype or null - */ - public static ScoreModelI getScoreModel(String pwtype) - { - return scoreMatrices.get(pwtype); - } - public static float getPAM250(char c, char d) { int a = aaIndex[c];